FOR SHAREPOINT ON-PREMISE AS TARGET:
For SharePoint On-Prem as target we have an entry called 'EnableNestedContentsReportActions' in ApplicationSettings.xml file under %appadata%\Roaming\Metalogix\Content Matrix Console - eRoom Edition which is set to false by default. You would need to change this setting to true.
<XmlableEntry>
<Key>EnableNestedContentsReportActions</Key>
<Value>True</Value>
</XmlableEntry>
Once this is set to true you can then control on migrating the eRoom contents based on its nested structure.
NOTE: For this you would need to connect the target at web-application level. And for this you need to have Metalogix Extension Web Service (MEWS) installed in your SharePoint server.
Once MEWS is installed connect the target at web application level (using farm admin account or web application admin account) and follow the steps that we discussed during our call.
FOR SHAREPOINT ONLINE AS TARGET:
For SPO as target unfortunately we cannot apply the same workaround. The above workaround is only for SharePoint On-Premise as target.